Variant report

Variant	rs1967559
Chromosome Location	chr4:57305699-57305700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:57305489-57305709	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57268050..57270580-chr4:57305183..57307241,2	K562	blood:
2	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:

Variant related genes	Relation type
PPAT	TF binding region
ENSG00000270109	Chromatin interaction
ENSG00000174780	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10008223	0.85[ASN][1000 genomes]
rs10013402	0.87[ASN][1000 genomes]
rs10017460	0.86[ASN][1000 genomes]
rs10051	0.87[ASN][1000 genomes]
rs10434444	0.83[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs10434445	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1060472	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11133442	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11133443	0.83[TSI][hapmap]
rs12498340	0.83[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]
rs12501334	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12501502	1.00[CEU][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12503412	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12504291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12505767	0.84[ASN][1000 genomes]
rs12505939	0.87[ASN][1000 genomes]
rs12508008	0.90[ASW][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.89[ASN][1000 genomes]
rs12509542	0.89[ASN][1000 genomes]
rs12510712	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12511770	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12513091	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12646703	0.84[MEX][hapmap]
rs12646890	0.89[ASN][1000 genomes]
rs13147900	0.90[JPT][hapmap]
rs1356787	0.84[MEX][hapmap]
rs1401904	0.90[JPT][hapmap]
rs1401906	0.90[JPT][hapmap]
rs14211	0.90[ASW][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.87[ASN][1000 genomes]
rs1474179	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1520026	1.00[CEU][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1520030	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17086696	0.86[CHD][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.87[ASN][1000 genomes]
rs17086794	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17086832	0.85[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs17086853	0.90[ASW][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.89[ASN][1000 genomes]
rs1983378	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2030366	0.88[ASN][1000 genomes]
rs2271923	1.00[CEU][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28510634	0.85[ASN][1000 genomes]
rs28866881	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3796541	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3796548	0.83[TSI][hapmap]
rs4340842	0.90[ASW][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4346704	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4493603	1.00[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs4618376	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs4864579	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4864580	0.87[ASN][1000 genomes]
rs4864583	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4864585	0.84[ASN][1000 genomes]
rs4865092	0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4865103	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4865107	0.89[ASN][1000 genomes]
rs4865108	0.87[ASN][1000 genomes]
rs5010012	0.91[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55915354	0.87[ASN][1000 genomes]
rs56040009	0.87[ASN][1000 genomes]
rs56099714	0.89[ASN][1000 genomes]
rs56229630	0.81[ASN][1000 genomes]
rs56392224	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56887793	0.89[ASN][1000 genomes]
rs58151706	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58333131	0.81[ASN][1000 genomes]
rs6554345	0.90[JPT][hapmap]
rs6554358	0.90[ASW][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.87[ASN][1000 genomes]
rs6584	0.84[MEX][hapmap]
rs66810706	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66858948	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs66863699	0.89[ASN][1000 genomes]
rs6820314	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6821301	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6824893	0.86[ASN][1000 genomes]
rs6829250	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6830518	0.84[MEX][hapmap]
rs6832797	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6834696	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6834736	0.90[JPT][hapmap]
rs6836118	0.83[TSI][hapmap]
rs6846895	0.83[EUR][1000 genomes]
rs6849183	0.90[ASW][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6855041	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7664841	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7670991	0.83[ASN][1000 genomes]
rs8340	0.83[CHB][hapmap];0.86[CHD][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs9799864	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1967559	SRP72	cis	Esophagus Mucosa	GTEx
rs1967559	SRP72	cis	lymphoblastoid	seeQTL
rs1967559	SRP72	cis	parietal	SCAN
rs1967559	SRP72	Cis_1M	lymphoblastoid	RTeQTL
rs1967559	AASDH	cis	parietal	SCAN
rs1967559	SRP72	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57299200-57305800	Active TSS	H1 Cell Line	embryonic stem cell
2	chr4:57299200-57305800	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr4:57299200-57305800	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr4:57303000-57309000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:57303400-57330800	Weak transcription	Spleen	Spleen
6	chr4:57303800-57308400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr4:57303800-57326000	Weak transcription	Gastric	stomach
8	chr4:57303800-57331000	Weak transcription	Stomach Mucosa	stomach
9	chr4:57303800-57332000	Weak transcription	Small Intestine	intestine
10	chr4:57304000-57305800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:57304000-57306800	Enhancers	Liver	Liver
12	chr4:57304000-57312000	Weak transcription	Left Ventricle	heart
13	chr4:57304000-57315800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:57304000-57330000	Weak transcription	Pancreas	Pancrea
15	chr4:57304000-57330000	Weak transcription	Right Ventricle	heart
16	chr4:57304000-57331800	Weak transcription	Esophagus	oesophagus
17	chr4:57304200-57305800	Weak transcription	Brain Angular Gyrus	brain
18	chr4:57304200-57305800	Weak transcription	Fetal Thymus	thymus
19	chr4:57304200-57306400	Weak transcription	Fetal Muscle Leg	muscle
20	chr4:57304200-57307800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr4:57304200-57307800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:57304200-57308000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr4:57304200-57308000	Weak transcription	Placenta	Placenta
24	chr4:57304200-57308200	Weak transcription	Brain Hippocampus Middle	brain
25	chr4:57304200-57314600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr4:57304200-57314800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr4:57304200-57317400	Weak transcription	Thymus	Thymus
28	chr4:57304200-57318800	Weak transcription	Colon Smooth Muscle	Colon
29	chr4:57304200-57319200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr4:57304200-57331800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:57304400-57305800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:57304400-57305800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:57304400-57305800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:57304400-57305800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:57304400-57305800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr4:57304400-57305800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr4:57304400-57305800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr4:57304400-57305800	Weak transcription	Fetal Intestine Large	intestine
39	chr4:57304400-57305800	Weak transcription	HMEC	breast
40	chr4:57304400-57306000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr4:57304400-57306200	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr4:57304400-57306200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:57304400-57306200	Weak transcription	A549	lung
44	chr4:57304400-57306400	Weak transcription	Primary B cells from cord blood	blood
45	chr4:57304400-57306600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr4:57304400-57307000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr4:57304400-57307000	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr4:57304400-57307000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:57304400-57307200	Weak transcription	Primary T cells from cord blood	blood
50	chr4:57304400-57307400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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